SMTL ID : 6nbd.1

Human methemoglobin state 2 determined using single-particle cryo-EM at 200 keV

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 17 residues within 4Å: Chain A: Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:K.61, A:K.61, A:V.62, A:L.83, A:L.91, A:V.93, A:N.97, A:F.98, A:F.98, A:L.101, A:L.136 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58 Metal complexes: A:H.87 HEM.2: 15 residues within 4Å: Chain B: T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, H.92, L.96, N.102, F.103, L.106, L.141 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:F.42, B:K.66, B:V.67, B:F.71, B:F.71, B:L.88, B:L.96, B:N.102, B:F.103, B:L.106, B:L.106, B:L.141 Salt bridges: B:H.63, B:K.66, B:K.66 pi-Stacking: B:H.63 Metal complexes: B:H.92 HEM.3: 18 residues within 4Å: Chain C: T.39, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, N.97, F.98, L.101, V.132, L.136 23 PLIP interactions: 23 interactions with chain C, Hydrophobic interactions: C:T.39, C:Y.42, C:Y.42, C:F.43, C:F.43, C:K.61, C:K.61, C:V.62, C:A.65, C:L.83, C:L.91, C:N.97, C:F.98, C:F.98, C:L.101, C:V.132, C:L.136 Salt bridges: C:H.45, C:H.58, C:K.61 pi-Stacking: C:H.58, C:H.58 Metal complexes: C:H.87 HEM.4: 16 residues within 4Å: Chain D: T.38, F.41, F.42, H.63, K.66, A.70, F.71, L.88, L.91, H.92, L.96, N.102, F.103, L.106, V.137, L.141 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:F.42, D:F.71, D:F.71, D:L.88, D:L.91, D:L.96, D:N.102, D:L.106, D:L.106, D:V.137, D:L.141 Salt bridges: D:H.63, D:K.66, D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herzik Jr., M.A. et al., High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM. Nat Commun (2019)

Release Date

2019-02-13

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hemoglobin subunit alpha

Hemoglobin subunit beta

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